Archaic human ancestry in East Asia (Skoglund and Jakobsson 2011)

Interestingly, Reich et al. (2011) did not find evidence of substantial Denisova admixture in Eastern Eurasia, with the exception of the islands of the Southeast into Australasia. If I have any ideas on the possible discrepancy between the two, I'll add them here.

PNAS doi: 10.1073/pnas.1108181108

Archaic human ancestry in East Asia

Pontus Skoglund, and Mattias Jakobsson

Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia (“Denisovans”) and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome—a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.

6 comments:

1. The admixture event occurred in Island South East Asia, and admixed individuals are found principally there, with some also in surrounding areas via dispersal to Australia, the Philippines and parts of South East Asia mainland.

2. The admixture event occurred in East Asia, and the present East Asian population arrived there more recently - like from the Americas, Beringia or Northern Asia someplace.

Very interesting. Have a 'feeling' that in future further research will expand the 'universe' farther still and more genetic indicators will be found in our makeup from groups who survived the last glacial cycle 'out of Africa'.

How to reconcile "population differentiation, genetic di- versity, and frequencies of derived alleles correlate with distance from Africa (1, 3, 34, 35), which is in line with anatomically modern human expansion out from Africa (3, 21)" with the data in Fig. 1B that shows that Africans are closer to chimpanzees, while non-Africans are closer to Denisovans and Neanderthals. Chimpanzees are less "modern" that Denisovans and Neanderthals, plus the more derived alleles the population shows the more modern it is.

"East Asian (two-sided t test: P < 10−6) and Native American (P < 10−8) populations were found to be more similar to archaic hominins compared with European and Central/South Asian populations"

This study reaffirms the fact of peculiar proximity of Amerindians to Neanderthals. On Fig. 1B one Amerindian sample is way out in the Neanderthal direction compared with the other populations. Table S3 shows that Amerindian populations (Colombian, Karitiana) rank right after Papuan, Melanesian and Yizu and ahead of many other East Asians in terms of frequencies of derived Denisovan alleles.

This is a systemic phenomenon: basal X chromosome haplotype B006 detected in Neanderthals is most frequent in Amerindians, among modern human populations; Amerindians are high on blood group O and this is the blood group identified in two Neanderthal individuals; the genetically driven odontological feature, such as shovel-shaped incisors, are most frequent in Amerindians and they are highly frequent in Neanderthals and Asian Homo erectus.

This is especially surprising because there're no archaic hominins in America, hence if the intensity of admixture is proportionate to the frequency of those shared alleles (as it's supposed to be), then we would expect to find the highest frequencies in Europe and East Asia, not in America and Oceania. Since America and Oceania harbor the greatest linguistic diversity on the planet - languages being the defining feature of behavioral modernity - these associations between "easternmost" non-Africans (Amerindians and Oceanians) and archaic hominins start looking like traces of common descent and not admixture. Africans, on the other hand, may have developed their close proximity to the chimps from homoplasies and through admixture with yet-to-be-identified local pre-modern hominins.

Thetre is a third possibility: that the admixture actually occurred near where the Denisovan humans lived. The connecting link between that region and the islands beyond SE Asia has since been broken by the expansion of a non-Denisonva-admixed population.

"This study reaffirms the fact of peculiar proximity of Amerindians to Neanderthals. On Fig. 1B one Amerindian sample is way out in the Neanderthal direction compared with the other populations. Table S3 shows that Amerindian populations (Colombian, Karitiana) rank right after Papuan, Melanesian and Yizu and ahead of many other East Asians in terms of frequencies of derived Denisovan alleles".

Because, presumably, an element of the American population passed through the region of the Denisovans. But Native Americans also consist in part of non-admixed Northeast Asian populations.

I agree with Terry, here. As I posted elsewhere, the data seem to support the notion that the admixture event was pre-Toba. Following that, the admixed population became isolated in the extreme SE and would later become Papuan and Australian and part Oceanian. The remainder in South China and surrouindings, now reduced, simply saw their admixture diluted by continuing migrations East from the subcontinent - both along the coast (preserving more admixture all the way to Beringia and the Americas) and inland (Myanmar/adjacent China, and Southern Siberia - no admixture).

the more derived alleles the population shows the more modern it is

The paper shows that in regions where modern humans have variation, and Denisovans carry the derived (non-Neanderthal, non-Chimpanzee) allele, we have about a 50% percent chance to also carry that allele - with extremely little variation across the globe. This indicates to me that modern humans split off the line (very roughly) about the same time when Denisovans and Neanderthal split (and subsequent mutations and admixture play a much smaller role).

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